As a WMG subpage, all spoilers are unmarked as per policy. You Have Been Warned.
Half-Life 2 VR: But the AI is Self-Aware will have new (or old) cast members taking on the roles of various miscellaneous Rebels.
This includes NPCs like Sandy & Laszlo from HL2 and Sheckley & Griggs from Episode 2.
The major characters in Half-Life 2 VR: But the AI is Self-Aware will be played by various cast members, old and new.
Bubby will return in Half-Life 2 VR: But the AI is Self-Aware, assuming the role of Dr. Isaac Kleiner.
Dr. Isaac Kleiner's model is based off the balding glasses-wearing scientist model that Bubby uses, so it's likely that he would replace Dr. Isaac Kleiner. In-universe, the G-Man was intended to be a Director-type AI that would create Dynamic Difficulty for the player.
However, he's using his status as AI Director to keep the Science Team safe because he's grown attached to Tommy as a son of his (possibly, Tommy could share some code with the G-Man's AI) and wants to allow him safe passage to the ending. Additionally... Benrey is the G-Man's Flawed Prototype.
Rather than keep a reasonable balance as the AI Director, Benrey's AI would frequently go Off the Rails by physically blocking the player and trying to put them off from completing the game. Valve deemed this unacceptable and reassigned Benrey's AI to a random security guard and stripping him of most of his abilities. However, Benrey managed to re-acquire his Director privileges (likely due to a poor patch job), explaining the events of Act 4. Gordon really did have his dick out the whole time, as per Benrey's Motive Rant.
...but nobody noticed or said anything, because why would they?- Semi-confirmed. Word of God is that Gordon did have his dick out at the beginning of the series, but Benrey kneeled down and pushed it back into Gordon's pants when he randomly crouched in front of Gordon during their first meeting.
The line, "You've killed a lot of men, haven't you Gordon?" was meant for the player, not Gordon.
At that time, Gordon had only killed a few people. However, Dr. Coomer seems to know that Gordon isn't an AI, and as such likely knows he plays other games. He could have read his Steam statistics like Psycho Mantis, and deduced that the player has killed many NPC's over the years. Monika from Doki Doki Literature Club! is Harold P. Coomer's daughter
They're both tutorial characters who attack the player character because they Go Mad from the Revelation that this isn't reality. Besides, we don't know her last name, and HLVRAI and DDLC are both parodies of 90's video game genres. Dr. Coomer was originally supposed to be the tutorial NPC
In addition, he was supposed to die from a rope as soon as the tutorial ended. Tommy Coolatta would later grow into a fully fledged computer virus...
...and change his name to Spamton B. Spamton.